The first two names that people tend to think of when it comes to leaders of the X-Men are its founder, Professor Charles Xavier and a member of his first class of students, Cyclops. Of course, many others have stepped up to give orders throughout the franchise's decades-long run, but the majority of those individuals have been male.
Though it began in Marvel's ResurrXion publishing line, Marvel Legacy has seen a drastic shift in the X-Men's leadership department, with more women stepping to the forefront. And frankly, this change should have happened a long time ago. Not many comic book franchises have the deep roster of strong women characters and a rabid fanbase just dying to see their favorites elevated to new heights like the X-Men.
Marvel Legacy's progressive move was cemented with the original, adult Jean Grey returning from the dead in Phoenix Resurrection: The Return of Jean Grey and the launch of X-Men Red. There are now three ongoing X-Men titles with female leaders -- adult Jean Grey in X-Men Red, young Jean Grey in X-Men Blue and Kitty Pryde in X-Men Gold -- with Jubilee's role in the recently-canceled Generation X making it a fourth. When you count miniseries like Rogue & Gambit (with Rogue's name getting top billing) and New Mutants: Dead Souls (Magik bringing the team together) that number grows even larger, and is a concerted effort by the publisher to give fans something they haven't already seen.
In a "back to basics" approach ahead of Marvel Legacy, the X-Men line was relaunched with X-Men Gold featuring a classic lineup of familiar mutants -- Kitty Pryde, Old Man Logan (taking the place of the deceased Wolverine), Storm, Nightcrawler, Colossus and Rachel Grey as Prestige. Instead of Storm, who has led her own team in the past, Kitty Pryde was chosen to be the team's leader and has run with the assignment, establishing the X-Men as a public team on par with the Avengers.
This move towards Kitty didn't come out of thin air, however, and had been building for years after she assumed a mentor role with the time-displaced original team of All-New X-Men. From there, Kitty even took on the mantle of Star-Lord for the Guardians of the Galaxy while Peter Quill tried his hand at ruling Spartax. The spotlight will grow larger for Kitty this summer during the "wedding of the century" to Colossus.
Speaking of the original X-Men, they became the focal point in X-Men Blue with the added twist of Jean Grey being in charge over Cyclops. Since being plucked from the past to the present, each team member underwent a significant change, but none more than the potential Phoenix host. All-New X-Men saw Jean begin to explore her powers in new ways while also gaining confidence in herself, all attributes one would want in a leader.
When Magneto was believed to be dead to the world, it was Jean who decided to work alongside the Master of Magnetism in secret. Of course, her teammates weren't keen on the idea of working with their sworn enemy, but it's not the first time enemies have made strange bedfellows in the world of the X-Men.